Author: scooter
Date: 2011-06-03 16:39:57 -0700 (Fri, 03 Jun 2011)
New Revision: 25636
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/FeatureVector/FeatureVectorCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
Log:
Removed some debugging and added a method in FeatureVectorCluster for creating
an edge
without going through Cytoscape.getCyEdge. This resulted in an
order-of-magnitude improvement
in the performance.
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/FeatureVector/FeatureVectorCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/FeatureVector/FeatureVectorCluster.java
2011-06-03 23:10:40 UTC (rev 25635)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/FeatureVector/FeatureVectorCluster.java
2011-06-03 23:39:57 UTC (rev 25636)
@@ -47,7 +47,9 @@
import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
import cytoscape.layout.Tunable;
+import cytoscape.layout.TunableListener;
import cytoscape.logger.CyLogger;
import cytoscape.task.TaskMonitor;
@@ -60,7 +62,7 @@
// clusterMaker imports
-public class FeatureVectorCluster extends AbstractClusterAlgorithm {
+public class FeatureVectorCluster extends AbstractClusterAlgorithm implements
TunableListener {
/**
* Linkage types
*/
@@ -80,10 +82,12 @@
boolean selectedOnly = false;
boolean zeroMissing = false;
boolean createEdges = false;
+ double edgeCutoff = 0.5;
String dataAttributes = null;
String edgeAttribute = null;
TaskMonitor monitor = null;
CyLogger logger = null;
+ final static String interaction = "distance";
public FeatureVectorCluster() {
super();
@@ -146,10 +150,18 @@
Tunable.BOOLEAN, new
Boolean(true)));
// Whether to create a new network or add values to existing
network
- clusterProperties.add(new Tunable("createEdges",
- "Create edges if they don't
exist",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable t = new Tunable("createEdges",
+ "Create edges if they don't exist",
+ Tunable.BOOLEAN, new Boolean(false));
+ t.addTunableValueListener(this);
+ clusterProperties.add(t);
+ // If we're creating edges, do we have a cut-off value?
+ t = new Tunable("edgeCutoff", "Only create edges if nodes are
closer than this",
+ Tunable.DOUBLE, new Double(0.5));
+ t.setImmutable(true);
+ clusterProperties.add(t);
+
clusterProperties.add(new Tunable("advancedParametersGroup",
"Advanced Parameters",
Tunable.GROUP, new
Integer(3),
@@ -174,6 +186,17 @@
updateSettings(false);
}
+ public void tunableChanged(Tunable tunable) {
+ if (tunable.getName().equals("createEdges")) {
+ createEdges = ((Boolean)
tunable.getValue()).booleanValue();
+ Tunable t = clusterProperties.get("edgeCutoff");
+ if (createEdges)
+ t.setImmutable(false);
+ else
+ t.setImmutable(true);
+ }
+ }
+
public void updateSettings(boolean force) {
clusterProperties.updateValues();
super.updateSettings(force);
@@ -203,6 +226,10 @@
if ((t != null) && (t.valueChanged() || force))
createEdges = ((Boolean) t.getValue()).booleanValue();
+ t = clusterProperties.get("edgeCutoff");
+ if ((t != null) && (t.valueChanged() || force))
+ edgeCutoff = ((Double) t.getValue()).doubleValue();
+
}
public void doCluster(TaskMonitor monitor) {
@@ -224,14 +251,19 @@
// To make debugging easier, sort the attribute array
Arrays.sort(attributeArray);
- if (monitor != null)
+ if (monitor != null) {
+ monitor.setPercentCompleted(0);
monitor.setStatus("Initializaing");
+ }
// Create the matrix
Matrix matrix = new Matrix(attributeArray, false,
ignoreMissing, selectedOnly);
- if (monitor != null)
+ if (monitor != null) {
+ monitor.setPercentCompleted(1);
monitor.setStatus("Calculating edge distances");
+ if (canceled) return;
+ }
// Create a weight vector of all ones (we don't use individual
weighting, yet)
matrix.setUniformWeights();
@@ -245,67 +277,103 @@
CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
// For each node, get the distance to all other nodes
+ double maxdistance = 0.0;
+ double mindistance = 0.0;
+
+ double distanceMatrix[][] = new double[nNodes][nNodes];
+ for (int i = 0; i < nNodes; i++) {
+ for (int j = i+1; j < nNodes; j++) {
+ double distance =
distanceMetric.getMetric(matrix, matrix, matrix.getWeights(), i, j);
+ maxdistance = Math.max(maxdistance, distance);
+ mindistance = Math.min(mindistance, distance);
+ distanceMatrix[i][j] = distance;
+ }
+ if (monitor != null) {
+ if (canceled) return;
+ monitor.setPercentCompleted((int)(25 *
(double)i/(double)nNodes));
+ }
+ }
+
+ if (monitor != null) {
+ monitor.setStatus("Assigning values to edges");
+ }
+
int[] nodeArray = new int[2];
- double maxweight = 0.0;
- double minweight = 0.0;
Map<CyEdge, Double> edgeList = new HashMap<CyEdge, Double>();
+ double scale = maxdistance - mindistance;
+ /* Performance tuning -- what's taking all the time!
+ long time = System.currentTimeMillis();
+ long nodeFetchTime = 0L;
+ long edgeFetchTime = 0L;
+ long edgeCreateTime = 0L;
+ long networkAddTime = 0L;
+ long setAttributeTime = 0L;
+ int newEdges = 0;
+ */
+
for (int i = 0; i < nNodes; i++) {
for (int j = i+1; j < nNodes; j++) {
- double weight =
distanceMetric.getMetric(matrix, matrix, matrix.getWeights(), i, j);
- maxweight = Math.max(maxweight, weight);
- minweight = Math.min(minweight, weight);
-
+ // time = System.currentTimeMillis();
+ double distance = distanceMatrix[i][j]/scale;
CyNode source =
Cytoscape.getCyNode(matrix.getRowLabel(i));
CyNode target =
Cytoscape.getCyNode(matrix.getRowLabel(j));
nodeArray[0] = source.getRootGraphIndex();
nodeArray[1] = target.getRootGraphIndex();
+ // nodeFetchTime +=
System.currentTimeMillis()-time;
+
+ if (createEdges == true && distance >
edgeCutoff)
+ continue;
+
+ // time = System.currentTimeMillis();
+
CyEdge edge;
int[] edgeArray =
network.getConnectingEdgeIndicesArray(nodeArray);
+ // edgeFetchTime +=
System.currentTimeMillis()-time;
+ // time = System.currentTimeMillis();
+
if ((edgeArray == null || edgeArray.length ==
0) && createEdges == true) {
- edge = Cytoscape.getCyEdge(source,
target, "interaction", "distance", true);
+ edge = myCreateEdge(source, target,
edgeAttributes);
+
+ // edgeCreateTime +=
System.currentTimeMillis()-time;
// System.out.println("Creating edge
between "+source+" and "+target);
if (edge != null) {
// System.out.println("Adding
edge "+edge.getIdentifier()+" to network");
+ // time =
System.currentTimeMillis();
network.addEdge(edge);
+ // networkAddTime +=
System.currentTimeMillis()-time;
}
} else if (edgeArray == null ||
edgeArray.length == 0) {
continue;
} else {
edge =
(CyEdge)network.getEdge(edgeArray[0]);
+ // edgeFetchTime +=
System.currentTimeMillis()-time;
}
if (edge == null) continue;
-
- edgeList.put(edge, new Double(weight));
-
+ // time = System.currentTimeMillis();
+
edgeAttributes.setAttribute(edge.getIdentifier(), edgeAttribute, distance);
+ // setAttributeTime +=
System.currentTimeMillis()-time;
}
+ if (monitor != null) {
+ if (canceled) return;
+ monitor.setPercentCompleted((int)(25 + (75 *
(double)i/(double)nNodes)));
+ }
}
- double scale = maxweight - minweight;
- // System.out.println("scale: "+maxweight+"-"+minweight+" =
"+scale);
+ /*
+ System.out.println("Created "+newEdges+" edges");
+ System.out.println("Edge creation time: "+edgeCreateTime+"ms");
+ System.out.println("Network add time: "+networkAddTime+"ms");
+ System.out.println("Edge fetch time: "+edgeFetchTime+"ms");
+ System.out.println("Node fetch time: "+nodeFetchTime+"ms");
+ System.out.println("Set attribute time:
"+setAttributeTime+"ms");
+ */
- for (CyEdge edge: edgeList.keySet()) {
- edgeAttributes.setAttribute(edge.getIdentifier(),
edgeAttribute, edgeList.get(edge)/scale);
- }
+ if (monitor != null)
+ monitor.setStatus("Complete");
-/*
- if (metric == DistanceMetric.EUCLIDEAN || metric ==
DistanceMetric.CITYBLOCK) {
- // Normalize distances to between 0 and 1
- double scale = 0.0;
- for (int node = 0; node < nodeList.length; node++) {
- if (nodeList[node].getDistance() > scale) scale
= nodeList[node].getDistance();
- }
- if (scale != 0.0) {
- for (int node = 0; node < nodeList.length;
node++) {
- double dist =
nodeList[node].getDistance();
- nodeList[node].setDistance(dist/scale);
- }
- }
- }
-*/
-
// Tell any listeners that we're done
pcs.firePropertyChange(ClusterAlgorithm.CLUSTER_COMPUTED, null,
this);
}
@@ -315,6 +383,27 @@
return false;
}
+ /**
+ * Cytoscape doesn't provide us with an easy way to create an edge
without searching
+ * for it first. Since we've already searched for it, we are
absolutely certain
+ * by this point that the edge doesn't exist, so we can save
significant time by
+ * just going ahead and creating it.
+ */
+ private CyEdge myCreateEdge(CyNode source, CyNode target, CyAttributes
edgeAttributes) {
+ int rootEdge = Cytoscape.getRootGraph().createEdge(source,
target);
+ CyEdge edge = (CyEdge)
Cytoscape.getRootGraph().getEdge(rootEdge);
+
+ // create the edge id
+ String edge_name =
CyEdge.createIdentifier(source.getIdentifier(),
+ interaction,
+
target.getIdentifier());
+ edge.setIdentifier(edge_name);
+
+ edgeAttributes.setAttribute(edge_name, Semantics.INTERACTION,
interaction);
+ edgeAttributes.setAttribute(edge_name,
Semantics.CANONICAL_NAME, edge_name);
+ return edge;
+ }
+
private String[] getAttributeArray(String dataAttributes) {
String indices[] = dataAttributes.split(",");
String selectedAttributes[] = new String[indices.length];
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2011-06-03 23:10:40 UTC (rev 25635)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2011-06-03 23:39:57 UTC (rev 25636)
@@ -195,11 +195,14 @@
return;
}
+ if (canceled) return;
+
//Cluster the nodes
runMCL = new RunMCL(matrix, inflation_parameter, rNumber,
clusteringThresh, maxResidual, maxThreads,
logger);
runMCL.setDebug(debug);
+
if (canceled) return;
// results = runMCL.run(monitor);
@@ -226,6 +229,7 @@
public void halt() {
canceled = true;
- runMCL.halt();
+ if (runMCL != null)
+ runMCL.halt();
}
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-06-03 23:10:40 UTC (rev 25635)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-06-03 23:39:57 UTC (rev 25636)
@@ -293,10 +293,10 @@
HashMap<CyEdge,CyEdge> edgeMap = new HashMap();
for (CyEdge edge: (List<CyEdge>)parentNet.edgesList()) {
- System.out.print("Edge: "+edge.getIdentifier());
+ // System.out.print("Edge: "+edge.getIdentifier());
// Is this a non-clustered edge?
if (!nodeMap.containsKey((CyNode)edge.getSource()) &&
!nodeMap.containsKey((CyNode)edge.getTarget())) {
- System.out.println(" Non-clustered");
+ // System.out.println(" Non-clustered");
continue;
}
@@ -305,10 +305,10 @@
// Is this an internal edge?
if (nodeMap.containsKey((CyNode)edge.getSource()) &&
nodeMap.containsKey((CyNode)edge.getTarget())) {
if (nodeMap.get(edge.getSource()) ==
nodeMap.get(edge.getTarget())) {
- System.out.println(" Internal only");
+ // System.out.println(" Internal only");
continue;
}
- System.out.println(" inter-cluster");
+ // System.out.println(" inter-cluster");
interaction = "inter-cluster";
} else {
interaction =
"cluster-"+edgeAttributes.getStringAttribute(edge.getIdentifier(),
Semantics.INTERACTION);
@@ -326,7 +326,7 @@
// Now create the new edge
CyEdge newEdge = Cytoscape.getCyEdge(source, target,
Semantics.INTERACTION, interaction, true);
- System.out.println("Adding "+newEdge.getIdentifier()+"
to parent network");
+ // System.out.println("Adding
"+newEdge.getIdentifier()+" to parent network");
// Add it to the parent network
parentNet.addEdge(newEdge);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-06-03 23:10:40 UTC (rev 25635)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-06-03 23:39:57 UTC (rev 25636)
@@ -282,10 +282,10 @@
continue;
}
if (!clusterMap.containsKey(cluster)) {
- System.out.println("Creating new entry
for: "+cluster.toString());
+ // System.out.println("Creating new
entry for: "+cluster.toString());
clusterMap.put(cluster, new
ArrayList<CyNode>());
}
- System.out.println("Adding node "+node+" to
"+cluster.toString());
+ // System.out.println("Adding node "+node+" to
"+cluster.toString());
clusterMap.get(cluster).add(node);
net.addNode(node);
}
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